Difference between revisions of "Sandbox"

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* '''Description:''' write here <br/><br/>
+
* '''Description:''' similar to NifS protein homolog <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pcp''
+
|''ycbU''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
Line 10: Line 10:
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || pyrrolidone-carboxylate peptidase (EC 3.4.11.8)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' ||  
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23 kDa, 6.418  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 6.455  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 645 bp, 215 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1110 bp, 370 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[tatCD]]'', ''[[ycbU]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pcp]]'', ''[[lmrB]]''
 
|-
 
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12059&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12060&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:pcp_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:ycbU_context.gif]]
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
Line 41: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ycbU.html]
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10873]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11176]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 56:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
* '''Protein family:'''
+
* '''Protein family:''' class-V pyridoxal-phosphate-dependent aminotransferase family
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 72: Line 74:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
* '''Localization:''' Cytoplasm
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU02650]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU02660]
  
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.4.11.8 3.4.11.8]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===

Revision as of 17:43, 21 April 2009

  • Description: similar to NifS protein homolog

Gene name ycbU
Synonyms
Essential no
Product unknown
Function unknown
MW, pI 40 kDa, 6.455
Gene length, protein length 1110 bp, 370 aa
Immediate neighbours pcp, lmrB
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YcbU context.gif
This image was kindly provided by SubtiList





The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: class-V pyridoxal-phosphate-dependent aminotransferase family
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

  1. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed